Molecular modeling generally consists of two fields: physical molecular modeling tool kits and the resulting physical models, and computer-based molecular visualization and simulation software (i.e., virtual modeling).
Physical modeling tool kits allow a person to build a physical representation, e.g., of the atomic structure of a molecule. These molecular modeling tool kits consist of hardware elements, usually spherical, that represent individual atoms and other hardware elements, usually rod-shaped, that represent bonds between atoms. Molecular modeling tool kit users can construct a physical model that demonstrates the static properties of a particular molecular structure, such as the atomic structure and the distance between atoms.
Physical modeling tool kits such as these are static and non-interactive. The resulting three-dimensional (“3-D”) physical model cannot represent characteristics of the system that are not obvious to the human eye, such as the energetics of the system. Further, such models cannot represent the dynamic characteristics of the molecular system when it is in a changing environment such as shifting loads, stresses, or molecular and atomic interactions. Changing experimental variables also are not readily modeled, such as varying wind loads on a truss, bridge, or civil structure. Finally, molecular modeling tool kits and physical models do not computationally process or represent a virtual model of the subject matter on a computer screen.
Virtual software tools allow a user to create a virtual model, e.g., a molecule on a computer, to visualize the atomic structure and to simulate the characteristics of the molecular system. Examples of such commercially available software tools include Insight II, available from Accelrys (www.accelrys.com), and Virtual Molecular Dynamics (University of Chicago). Some such software tools are capable of representing the molecular structure, analyzing the molecular energetics, and simulating changes within the molecule or interactions with other molecules. Some software tools incorporate quantum mechanical effects, either by semi-empirical methods or using actual ab initio methods.
Unfortunately, although state-of-the-art visualization and simulation software is sufficiently powerful to simulate a molecular or other structure, it is difficult to obtain the geometry of choice by manipulating a virtual model on the computer screen. The user input interface in both creating the virtual model or in modifying that model for simulation is generally limited to the keyboard/mouse or a similar human-computer interface. The user can control only one parameter at a time, such as the rotation of a dihedral angle or the addition of a new atom. This process is unintuitive and time consuming.
Rather, it is more intuitive and faster to manipulate by hand a physical 3-D physical model, conforming it to the geometry of choice. However, such physical models are static and are not capable of simulating complex characteristics of the resulting structure. Even after the preferred geometry is obtained, only limited useful information can be obtained without a computer and the appropriate visualization and simulation software.
What is needed is a modeling system that includes the benefits of both physical and virtual modeling systems. Such a hybrid modeling system should include the speed and ease-of-use characteristics of physical models, and also include the advanced computational and visualization tools available in computer-based virtual modeling programs.